domains / families / science / annotation-qc

annotation-qc

separate

Assesses the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk (proteome completeness, consistency, and contamination), CheckM2 (prokaryotic completeness/contamination), and a gene-set sanity panel (gene count, mono-exonic fraction, protein-length distribution, mRNA:gene ratio, coding density). Covers the assembly-BUSCO-vs-proteome-BUSCO diagnostic, what BUSCO-Duplicated really means, why gene count is a vanity metric, and the QC of transferred annotations. Use when judging whether an annotation is good enough to publish or submit, diagnosing a suspect annotation, or comparing annotation completeness across pipelines.

When to use

• judging whether an annotation is good enough to publish
• diagnosing a suspect annotation
• comparing annotation completeness across pipelines
• assessing prokaryotic genome/MAG quality
• assessing eukaryotic annotation quality
• QC of transferred annotations
• diagnosing high gene count
• diagnosing high BUSCO-Duplicated

When not to use

• fixing the assembly
• running BUSCO on genome mode reported as if it described the annotation

Skill page

Source